Over recent years, many publications have reported the use of phage-display technology to produce and screen libraries of polypeptides for binding to a selected target. See, e.g, Cwirla, et al., Proc. Natl. Acad. Sci. USA 87:6378-6382 (1990); Devlin, et al., Science 249:404-406 (1990), Scott and Smith, Science 249:386-388 (1990); Ladner, et al., U.S. Pat. No. 5,571,698. A basic concept of phage display methods is the establishment of a physical association between DNA encoding a polypeptide to be screened and the polypeptide. This physical association is provided by the phage particle, which displays a polypeptide as part of a capsid enclosing the phage genome which encodes the polypeptide. The establishment of a physical association between polypeptides and their genetic material allows simultaneous mass screening of very large numbers of phage bearing different polypeptides. Phage displaying a polypeptide with affinity to a target bind to the target and these phage are enriched by affinity screening to the target. The identity of polypeptides displayed from these phage can be determined from their respective genomes. Using these methods a polypeptide identified as having a binding affinity for a desired target can then be synthesized in bulk by conventional means.
Phage display technology has also been used to produce and screen libraries of heterodimeric proteins, such as Fab fragments. See e.g., Garrard, et al., Bio/Tech 9:1373-1377 (1991). Phage display libraries of Fab fragments are produced by expressing one of the component chains as a fusion with a coat protein, as for display of single-chain polypeptides. The partner antibody chain is expressed in the same cell from the same or a different replicon as the first chain, and assembly occurs within the cell. Thus, a phage-Fab fragment has one antibody chain fused to a phage coat protein so that it is displayed from the outer surface of the phage and the other antibody chain is complexed with the first chain.
In a further expansion of the basic approach, polypeptide libraries have been displayed from replicable genetic packages other than phage. These replicable genetic packages include eukaryotic viruses and bacteria. The principles and strategy are closely analogous to those employed for phage, namely, that nucleic acids encoding antibody chains or other polypeptides to be displayed are inserted into the genome of the package to create a fusion protein between the polypeptides to be screened and an endogenous protein that is exposed on the cell or viral surface. Expression of the fusion protein and transport to the cell surface result in display of polypeptides from the cell or viral surface.
Although conventional display methods have achieved considerable success in isolating antibodies and other polypeptides with specific binding to selected targets, some inefficiencies and limitations remain. In conventional methods, many library members bind nonspecifically to the target or the solid phase bearing the target and are amplified along with specifically bound library members causing poor efficiency at each round of affinity selection. Not only can this waste time and effort in performing many rounds of affinity selection, but members bearing polypeptides having specific affinity are lost at each round. Selection is generally terminated when sufficient rounds of affinity selection have been performed to achieve a significant number of members bearing polypeptides with affinity for a target even though many nonspecifically binding members are still present. Clonal isolates are then picked and tested individually to reduce the risk of losing specific-binding members through further rounds of selection. Clonal isolates shown to bind specifically may then be cloned into an expression work for future analysis, and, large-scale production. Accordingly, only one or a few of library members bearing polypeptides with specific affinity for the target present in the original repertoire are ever isolated.
The present application provides inter alia novel methods that overcome these inefficiencies and difficulties, and produce new diagnostic and therapeutic reagents.
The invention provides libraries of at least four chimeric antibodies. At least 50% of the antibodies in the library have specific affinity for the same target and no library member constitutes more than 25% of the library. In some libraries, the antibodies are Fab fragments. In some libraries, the antibodies are single-chain antibodies. In some libraries, the antibodies are intact antibodies. Typically, a chimeric antibody light chain comprises a nonhuman light chain variable region and a human light chain constant region. Typically, a chimeric antibody heavy chain comprises a nonhuman heavy chain variable region and a human heavy chain constant region. In some libraries at least some antibodies have light and heavy chain variable regions that are randomly associated.
The invention further provides libraries of at least four different nucleic segments encoding chimeric antibody chains comprising a variable region and a constant region from different species. At least 90% of segments in the library encode chimeric antibody chains showing specific affinity for the same target and no library member constitutes more than 50% of the library. Some such libraries comprise at least four pairs of the different nucleic acid segments, the members of a pair respectively encoding heavy and light chimeric antibody chains, wherein at least 90% of the pairs encode heavy and light chimeric antibody chains that form complexes showing specific affinity for the same target, and no pair of nucleic acid segments constitutes more than 50% of the library. In some libraries, at least 95% of library members encode chimeric antibody chains forming complexes having specific affinity for the target and no member constitutes more than 25% of the library. Some libraries have at least 100 different members. In some libraries, each pair of nucleic acids is expressed as a discistronic transcript.
The invention further provides methods of producing a polypeptide library having affinity for a target. Such methods entail providing a library of replicable genetic packages, wherein a member comprises a replicable genetic package capable of displaying an antibody chain encoded by a genome of the package and the antibody chain varying between members. One then subclones a mixed population of DNA molecules encoding at least four different antibody chains of the library of replicable genetic packages into multiple copies of an expression vector to produce modified forms of the expression vector. One then introduces the modified forms of the expression vector into a host and expressing the antibody chains as chimeric antibody chains in the host, wherein a library of at least four different chimeric antibody chains are expressed, at least 90% of modified forms of the expression vector encode chimeric antibody chains having specific affinity for a target and no modified form of the expression vector constitutes more than 50% of the total forms.
The invention further provides methods of producing an antibody library having affinity for a target as follows. A library of phage is provided in which a member of the library comprises a phage capable of displaying from its outersurface an antibody comprising an antibody heavy chain variable domain complexed with an antibody light chain variable domain, in which either the heavy or light chain variable domain is expressed as a fusion protein with a coat protein of the phage and the heavy and light chain variable domains are encoded by the genome of the phage, and the heavy and light chain varies between members. A mixture of DNA molecules encoding the heavy and light chain variable domains from the phage library members are subcloned into an expression vector to produce modified forms of the expression vector. The modified forms of the expression vector are then into a host and expressed to produce the heavy and light chain variable domains as chimeric heavy and light chains, which complex as chimeric antibodies. The antibodies are released from the host to form an antibody library of at least four antibodies in which at least 90% of modified forms of the expression vector encode antibodies with specific affinity for a target and no modified form of the expression vector constitutes more than 50% of the total forms.
The invention further provides method of enriching a polypeptide display library. Such methods entail providing a library of replicable genetic packages, in which a member comprises a replicable genetic package capable of displaying from its outersurface an antibody chain to be screened and a tag fused to the polypeptide or to a binding partner of the antibody chain, if present, which antibody chain is encoded by a segment of a genome of the package. The antibody chains varies between library members. The number of copies of the antibody chain and/or the binding partner (if present) displayed per library member varies between library members, and the tag is the same in different library members. The antibody chain is a chimeric antibody chain comprising a variable region from a first species and a constant region from a second species. The library is then contacted with a receptor having a specific affinity for the tag under conditions in which library members displaying the antibody chain or the binding partner fused to the tag are bound to immobilized receptor. Library members bound to the immobilized receptor are separated from unbound library members to produce a sublibrary enriched relative to the library for members displaying the antibody chain or the binding partner.
The invention further provides methods of enriching a Fab phage display library. Such methods entail providing a library of phage in which a library member comprises a phage capable of displaying from its outersurface a fusion protein comprising a phage coat protein, a chimeric antibody light or heavy chain comprising a variable region and a constant region from different species, and a tag, wherein in at least some members, the chimeric antibody heavy or light chain is complexed with a partner chimeric antibody heavy or light chain domain chain, comprising a variable region and a constant region from the different species, the complex forming a Fab fragment to be screened, wherein the fusion protein and/or the partner chimeric antibody heavy or light chain are encoded by segment(s) of the genome of the phage, and the number of copies of the fusion protein and the partner chimeric antibody chain displayed per phage vary between library members. The library or a fraction thereof is contacted with a receptor having a specific affinity for the tag whereby library members displaying a copy of the fusion protein are bound to immobilized receptor by bonding between the receptor and the tag. Library members bound to the receptor are separated from unbound library members to produce an sublibrary enriched relative to the library for members displaying the fusion protein.
The invention further provides a method of enrich a phage display library as follows.
A library of phage is provided in which a library member comprises a phage capable of displaying from its outersurface a fusion protein comprising a phage coat protein, and a chimeric antibody heavy or light chain comprising a heavy or light chain variable region from a first species and a heavy or light chain constant region from a second species, wherein in at least some members, the chimeric antibody heavy or light chain is complexed with a partner chimeric antibody heavy or light chain comprising a heavy or light chain variable region from the first species and a heavy or light chain constant region from the second species, the partner being fused to a tag, the complex forming a chimeric Fab fragment to be screened, wherein the fusion protein and/or the partner chimeric antibody heavy or light chain fused to the tag are encoded by segment(s) of the genome of the phage, and the number of copies of the fusion protein and the partner chimeric antibody chain displayed per phage vary between library members. The library or a faction thereof is contacted with a receptor having a specific affinity for the tag under conditions whereby library members displaying the partner chimeric antibody chain are bound to immobilized receptor by binding between the immobilized receptor and the tag. Library members bound to the receptor are separated from unbound library members to produce an sublibrary enriched relative to the library for members displaying the partner chimeric antibody chain.
In another aspect, the invention provides methods of producing a multivalent polypeptide display library. The starting material is a library of replicable genetic packages, such as phage. A member of such a library is capable of displaying from its outer surface a fusion protein comprising a polypeptide to be screened and a tag. The fusion protein is encoded by a segment of a genome of the package. The polypeptides vary between library members, as does the number of copies of the fusion protein displayed per library member. The tag is the same in different library members. The library is contacted with a receptor having a specific affinity for the tag under conditions whereby library members displaying at least two copies of the fusion protein are preferentially bound to immobilized receptor by multivalent bonds between the receptor and the at least two copies of the tag. Library members bound to the immobilized receptor are then separated from unbound library members to produce a sublibrary enriched relative to the library for members displaying at least two copies of the fusion protein.
Polypeptides of particular interest are antibodies, particularly Fab fragments. Multivalent Fab phage display libraries can be produced as follows. The starting material is a library of phage in which a library member comprises a phage capable of displaying from its outer surface a fusion protein comprising a phage coat protein, an antibody light or heavy chain variable domain, and a tag. In at least some members, the antibody heavy or light chain is complexed with a partner antibody heavy or light chain variable domain chain, the complex forming a Fab fragment to be screened. The fusion protein and/or the partner antibody heavy or light chain are encoded by segment(s) of the genome of the phage. The number of copies of the fusion protein and the partner antibody chain displayed per phage vary between library members. The library or a fraction thereof is contacted with a receptor having a specific affinity for the tag under conditions whereby library members displaying at least two copies of the fusion protein are preferentially bound to immobilized receptor by multivalent bonds between the receptor and the at least two copies of the tag. Library members bound to the receptor are then separated from unbound library members to produce a sublibrary enriched relative to the library for members displaying at least two copies of the fusion protein.
An alternative method of producing a multivalent Fab phage display library is as follows. The starting material is a library of phage in which a library member comprises a phage capable of displaying from its outer surface a fusion protein comprising a phage coat protein, and an antibody light or heavy chain variable domain. At least in some members, the antibody light or heavy chain is complexed with a partner antibody heavy or light chain variable domain chain fused to a tag, the complex forming a Fab fragment to be screened. The fusion protein and/or the partner antibody heavy or light chain fused to the tag are encoded by segment(s) of the genome of the phage. The number of copies of the fusion protein and the partner antibody chain displayed per phage vary between library members. The library or a fraction thereof is contacted with a receptor having a specific affinity for the tag under conditions whereby library members displaying at least two copies of the partner antibody chain are preferentially bound to immobilized receptor by multivalent bonds between the immobilized receptor and the at least two copies of the tag. Bound library members are separated from unbound library members to produce an sublibrary enriched relative to the library for members displaying at least two copies of the partner antibody chain.
Having produced a polyvalent phage display library, such as described above, it can be screened by contacting the library with a target lacking specific affinity for the tag moiety(ies) and separating library members bound to the target via their displayed polypeptides from unbound library members.
DNA segments encoding polypeptides having specific affinity for a target can be subcloned in an expression vector, and the polypeptides expressed in host cells. Polypeptides can then, for example, be formulated with diagnostic or therapeutic excipients.
In another aspect, the invention provides libraries of nucleic acid segments encoding polyclonal polypeptides having specific affinity for a target. Such a library comprises least four different nucleic acid segments. At least 90% of segments in the library encode polypeptides showing specific affinity for a target and no library member constitutes more than 50% of the library. In some libraries, at least 95% of library members encode polypeptides having specific affinity for a target and no member constitutes more than 25% of the library. Some libraries have at least 100 different members. In some libraries, the segments are contained in a vector. In some libraries, the segment encode antibody chains. In some libraries, first and second segments are present, respectively encoding antibody heavy chains and partner antibody light chains, which can complex to form a Fab fragment. The first and second segments can be incorporated into the same or different vectors.
The invention further provides cell libraries in which a member cell contains a nucleic acid segment from a nucleic acid library, as described above. Such a library of cells can be propagated under conditions in which the DNA segments are expressed to produce polyclonal polypeptides.
The invention further provides methods of producing polyclonal polypeptides having specific affinity for a target. The starting material for such methods is a library of replicable genetic packages. A member comprises a replicable genetic package capable of displaying a polypeptide to be screened encoded by a genome of the package. The polypeptides vary between members. DNA encoding at least four different polypeptides of the library of replicable genetic packages is subcloned into an expression vector to produce modified forms of the expression vector. The modified forms of the expression vector are introduced into a host and expressed in the host producing at least four different polypeptides. At least 75% of modified forms of the expression vector encode polypeptides having specific affinity for a target and no modified form of the expression vector constitutes more than 50% of the total.
Polypeptides of particular interest are antibodies and these are typically displayed from phage libraries. A typical member of such a library is a phage capable of displaying from its outer surface an antibody comprising an antibody heavy chain variable domain complexed with an antibody light chain variable domain. Either the heavy or light chain variable domain is expressed as a fusion protein with a coat protein of the phage and either the heavy or light chain variable domain or both is/are encoded by the genome of the phage. The heavy and/or light chain varies between members. DNA encoding the heavy and/or light chain variable domains are subcloned from the phage library members into an expression vector to produce modified forms of the expression vector. The modified forms of the expression vector are introduced into a host and expressed to produce antibodies formed by the heavy and light chain variable domains of the phage library in the host. The antibodies are then released from the host to form an antibody library of at least four antibodies. At least 75% of modified forms of the expression vector encode antibodies with specific affinity for a target and no modified form of the expression vector constitutes more than 50% of the total.
Polyclonal libraries of antibodies and other polypeptides produced by the above methods can be incorporated into a diagnostic kit, or formulated for use as a diagnostic or therapeutic reagent.